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Zeng X, Su GP, Li SJ, Lv SQ, Wen ML, Li Y. Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning. BMC Bioinformatics 2024; 25:156. [PMID: 38641811 PMCID: PMC11031932 DOI: 10.1186/s12859-024-05783-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning, and design, as well as for understanding the functions of target. Although there are a few online platforms based on deep learning for drug-target interaction, affinity, and binding sites identification, there is currently no integrated online platforms for all three aspects. RESULTS Our solution, the novel integrated online platform Drug-Online, has been developed to facilitate drug screening, target identification, and understanding the functions of target in a progressive manner of "interaction-affinity-binding sites". Drug-Online platform consists of three parts: the first part uses the drug-target interaction identification method MGraphDTA, based on graph neural networks (GNN) and convolutional neural networks (CNN), to identify whether there is a drug-target interaction. If an interaction is identified, the second part employs the drug-target affinity identification method MMDTA, also based on GNN and CNN, to calculate the strength of drug-target interaction, i.e., affinity. Finally, the third part identifies drug-target binding sites, i.e., pockets. The method pt-lm-gnn used in this part is also based on GNN. CONCLUSIONS Drug-Online is a reliable online platform that integrates drug-target interaction, affinity, and binding sites identification. It is freely available via the Internet at http://39.106.7.26:8000/Drug-Online/ .
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Affiliation(s)
- Xin Zeng
- College of Mathematics and Computer Science, Dali University, Dali, 671003, China
| | - Guang-Peng Su
- College of Mathematics and Computer Science, Dali University, Dali, 671003, China
| | - Shu-Juan Li
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, 671000, China
| | - Shuang-Qing Lv
- Institute of Surveying and Information Engineering West, Yunnan University of Applied Science, Dali, 671000, China
| | - Meng-Liang Wen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650000, China
| | - Yi Li
- College of Mathematics and Computer Science, Dali University, Dali, 671003, China.
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Zhong KY, Wen ML, Meng FF, Li X, Jiang B, Zeng X, Li Y. MMDTA: A Multimodal Deep Model for Drug-Target Affinity with a Hybrid Fusion Strategy. J Chem Inf Model 2024; 64:2878-2888. [PMID: 37610162 DOI: 10.1021/acs.jcim.3c00866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The prediction of the drug-target affinity (DTA) plays an important role in evaluating molecular druggability. Although deep learning-based models for DTA prediction have been extensively attempted, there are rare reports on multimodal models that leverage various fusion strategies to exploit heterogeneous information from multiple different modalities of drugs and targets. In this study, we proposed a multimodal deep model named MMDTA, which integrated the heterogeneous information from various modalities of drugs and targets using a hybrid fusion strategy to enhance DTA prediction. To achieve this, MMDTA first employed convolutional neural networks (CNNs) and graph convolutional networks (GCNs) to extract diverse heterogeneous information from the sequences and structures of drugs and targets. It then utilized a hybrid fusion strategy to combine and complement the extracted heterogeneous information, resulting in the fused modal information for predicting drug-target affinity through the fully connected (FC) layers. Experimental results demonstrated that MMDTA outperformed the competitive state-of-the-art deep learning models on the widely used benchmark data sets, particularly with a significantly improved key evaluation metric, Root Mean Square Error (RMSE). Furthermore, MMDTA exhibited excellent generalization and practical application performance on multiple different data sets. These findings highlighted MMDTA's accuracy and reliability in predicting the drug-target binding affinity. For researchers interested in the source data and code, they are accessible at http://github.com/dldxzx/MMDTA.
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Affiliation(s)
- Kai-Yang Zhong
- College of Mathematics and Computer Science, Dali University, Dali 671003, China
| | - Meng-Liang Wen
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming 650000, China
| | - Fan-Fang Meng
- College of Mathematics and Computer Science, Dali University, Dali 671003, China
| | - Xin Li
- College of Mathematics and Computer Science, Dali University, Dali 671003, China
| | - Bei Jiang
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan, Dali University, Dali 671000, China
| | - Xin Zeng
- College of Mathematics and Computer Science, Dali University, Dali 671003, China
| | - Yi Li
- College of Mathematics and Computer Science, Dali University, Dali 671003, China
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Zeng X, Li SJ, Lv SQ, Wen ML, Li Y. A comprehensive review of the recent advances on predicting drug-target affinity based on deep learning. Front Pharmacol 2024; 15:1375522. [PMID: 38628639 PMCID: PMC11019008 DOI: 10.3389/fphar.2024.1375522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
Accurate calculation of drug-target affinity (DTA) is crucial for various applications in the pharmaceutical industry, including drug screening, design, and repurposing. However, traditional machine learning methods for calculating DTA often lack accuracy, posing a significant challenge in accurately predicting DTA. Fortunately, deep learning has emerged as a promising approach in computational biology, leading to the development of various deep learning-based methods for DTA prediction. To support researchers in developing novel and highly precision methods, we have provided a comprehensive review of recent advances in predicting DTA using deep learning. We firstly conducted a statistical analysis of commonly used public datasets, providing essential information and introducing the used fields of these datasets. We further explored the common representations of sequences and structures of drugs and targets. These analyses served as the foundation for constructing DTA prediction methods based on deep learning. Next, we focused on explaining how deep learning models, such as Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Transformer, and Graph Neural Networks (GNNs), were effectively employed in specific DTA prediction methods. We highlighted the unique advantages and applications of these models in the context of DTA prediction. Finally, we conducted a performance analysis of multiple state-of-the-art methods for predicting DTA based on deep learning. The comprehensive review aimed to help researchers understand the shortcomings and advantages of existing methods, and further develop high-precision DTA prediction tool to promote the development of drug discovery.
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Affiliation(s)
- Xin Zeng
- College of Mathematics and Computer Science, Dali University, Dali, China
| | - Shu-Juan Li
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Shuang-Qing Lv
- Institute of Surveying and Information Engineering West Yunnan University of Applied Science, Dali, China
| | - Meng-Liang Wen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Yi Li
- College of Mathematics and Computer Science, Dali University, Dali, China
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4
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Xu Y, Zhao JY, Geng Y, Yuan HR, Li LL, Wen ML, Li MG, Tang SK. Viridibacillus soli sp. nov., isolated from forest soil in Ailaoshan National Nature Reserve. Arch Microbiol 2021; 204:60. [PMID: 34940943 DOI: 10.1007/s00203-021-02676-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/30/2022]
Abstract
A Gram stain-positive, rod-shaped, and subterminal endospore-forming bacterium, designated strain YIM B01967T, was isolated from a forest soil sample collected in Ailaoshan National Nature Reserve, Yuxi City, Xinpin county, Yunnan province, China. Strain YIM B01967T showed the highest 16S rRNA gene sequence similarity with Viridibacillus arvi (99.1%) and Viridibacillus arenosi (98.9%). Based on the phylogenetic and 16S rRNA gene sequence results, strain YIM B01967T was affiliated to the genus Viridibacillus. The growth of YIM B01967T was observed at 15-35 °C (optimum, 28 °C), pH 7.0-9.0 (optimum, pH 7.5) and in the presence of 0-2% (w/v) NaCl (optimum in 2% NaCl). The cell wall sugars include ribose, glucose, arabinose, galactose, and mannose. The quinone system consisted of the major compound MK-8 and moderate amounts of MK-7. The major fatty acids (> 10%) included iso-C15:0, anteiso-C15:0, C16:1 ω10c. The major polar lipids profile included DPG, PME. The cell wall peptidoglycan was most likely of the type A4α with an L-Lys-D-Asp interpeptide bridge. The genomic DNA G + C content of strain YIM B01967T was 36.3 mol%. The ANI and digital DNA-DNA hybridization (dDDH) values between strain YIM B01967T and Viridibacillus arvi DSM 16317 T, Viridibacillus arenosi DSM 16319 T were 61.0% and 32.1%, 60.0% and 33.1% based on the draft genome sequence. The results support the conclusion that strain YIM B01967T represents a novel species of the genus Viridibacillus, for which the name Viridibacillus soli sp. nov., is proposed. The type strain is YIM B01967T (= KCTC 43249 T = CGMCC 1.18436 T).
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Affiliation(s)
- Yan Xu
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jiang-Yuan Zhao
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Yu Geng
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Hui-Ren Yuan
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Le-Le Li
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meng-Liang Wen
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ming-Gang Li
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China.
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Shi ZK, Gong XW, Zhao JY, Li MG, Han XL, Wen ML. Functional Characterization of a New Bifunctional Terpene Synthase LpNES1 from a Medicinal Plant Laggera pter odonta. J Oleo Sci 2021; 70:1641-1650. [PMID: 34645748 DOI: 10.5650/jos.ess21172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Laggera pterodonta, known in China as 'Choulingdan' for its stimulous odor, has long been used as traditional herbal medicine. The essential oil of L. pterodonta, which exhibits various pharmacological activities, is a rich resource of monoterpenes and sesquiterpenes. To date, however, the terpene synthases responsible for their production remain unknown. In present study, a new terpene synthase gene (LpNES1) was identified from L. pterodonta, transcript level of which was significantly upregulated in response to methyl jasmonate treatment. Recombinant LpNES1 could synthesize (E)-nerolidol and minor β-farnesene from farnesyl diphosphate and linalool from geranyl diphosphate in vitro. Whereas, only sesquiterpenes including (E)-nerolidol and minor β-farnesene were released when LpNES1 was reconstituted in yeast, even coexpressed with a geranyl diphosphate synthase (ERG20WW). Combined with subcellular localization experiment, the result indicated that the cytosol-targeted LpNES1 was responsible for (E)-nerolidol biosynthesis exclusively in L. pterodonta. Additionally, the expression level of LpNES1 gene was more prominent in floral buds than that in other tissues. LpNES1 characterized in present study not only lays the molecular foundation for sesquiterpene biosynthesis of L. pterodonta, but provides a key element for further biosynthesis of bioactive compound in microbes.
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Affiliation(s)
- Zhan-Ku Shi
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University
| | - Xiao-Wei Gong
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University.,R&D Center of China Tobacco Yunnan Industrial Co., Ltd
| | - Jiang-Yuan Zhao
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University
| | - Ming-Gang Li
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University
| | - Xiu-Lin Han
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University
| | - Meng-Liang Wen
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University
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Geng Y, Zhao JY, Yuan HR, Li LL, Wen ML, Li MG, Tang SK. Aestuariimicrobium ganziense sp. nov., a new Gram-positive bacterium isolated from soil in the Ganzi Tibetan autonomous prefecture, China. Arch Microbiol 2021; 203:2653-2658. [PMID: 33710378 DOI: 10.1007/s00203-021-02261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
A novel Gram-stain positive, oval-shaped, and non-flagellated bacterium, designated YIM S02566T, was isolated from alpine soil in Shadui Towns, Ganzi County, Ganzi Tibetan Autonomous Prefecture, Sichuan Province, PR China. Growth occurred at 23-35 °C (optimum, 30 °C) in the presence of 0.5-4% (w/v) NaCl (optimum, 1%) and at pH 7.0-8.0 (optimum, pH 7.0). The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain YIM S02566T was most closely related to the genus Aestuariimicrobium, with Aestuariimicrobium kwangyangense R27T and Aestuariimicrobium soli D6T as its closest relative (sequence similarities were 96.3% and 95.4%, respectively). YIM S02566T contained LL-diaminopimelic acid in the cell wall. MK-9(H4) was the predominant menaquinone. The major fatty acid patterns were anteiso-C15:0 (60.0%). The major polar lipid was DPG. The genome size of strain YIM S02566T was 3.1 Mb, comprising 3078 predicted genes with a DNA G + C content of 69.0 mol%. Based on these genotypic, chemotaxonomic and phenotypic evidences, strain YIM S02566T was identified as a novel species in the genus Aestuariimicrobium, for which the name Aestuariimicrobium ganziense sp. nov. is proposed. The type strain is YIM S02566T (= CGMCC 1.18751 T = KCTC 49,477 T).
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Affiliation(s)
- Yu Geng
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jiang-Yuan Zhao
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Hui-Ren Yuan
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Le-Le Li
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meng-Liang Wen
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ming-Gang Li
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Shu-Kun Tang
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
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Abstract
Forskolin is a complex labdane plant diterpenoid, which has been used in the treatment of a variety of diseases based on its activity as an activator of adenosine monophosphate(cAMP) cyclase. Natural forskolin exists only in the cork layer of the root of Coleus forskohlii. Due to the complexity of the extraction and chemical synthesis processes, the yield and purity of forskolin cannot meet commercial requirements. In recent years, with the rapid development of synthetic biology and the analysis and interpretation of many diterpene biosynthetic pathways, a new approach has been provided for the green production of forskolin. In this paper, the structure, activity, biosynthetic pathway and the heterologous biosynthesis of forskolin were reviewed. The problems and solutions in the heterologous biosynthesis of forskolin were also discussed and summarized, which will provide references for the construction of high-yielding forskolin engineering strains.
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Affiliation(s)
- Hui-Ren Yuan
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Institute of Microbiology, School of Life Sciences,Yunnan University Kunming 650091, China
| | - Ming-Gang Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Institute of Microbiology, School of Life Sciences,Yunnan University Kunming 650091, China
| | - Jiang-Yuan Zhao
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Institute of Microbiology, School of Life Sciences,Yunnan University Kunming 650091, China
| | - Meng-Liang Wen
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Institute of Microbiology, School of Life Sciences,Yunnan University Kunming 650091, China
| | - Xiu-Lin Han
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Institute of Microbiology, School of Life Sciences,Yunnan University Kunming 650091, China
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Ding ZG, Ding JH, Zhao JY, Chunyu WX, Li MG, Wang HB, Gu SJ, Wang F, Wen ML. A New Phenylspirodrimane Dimer Derivative from the Tin Mine Tailings-Associated Fungus Stachybotrys chartarum. Chem Nat Compd 2019. [DOI: 10.1007/s10600-019-02890-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ding ZG, Ding JH, Zhao JY, Li MG, Hu DB, Jiang XJ, Gu SJ, Wang F, Wen ML. Phenylspirodrimane Derivatives From Cultures of the Fungus Stachybotrys chartarum YIM DT 10079. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19878906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A new phenylspirodrimane derivative, stachartin F (1), and 2 known secondary metabolites stachybonoid E (2) and stachybonoid F (3) were isolated from cultures of the tin mine tailings-associated fungus Stachybotrys chartarum YIM DT 10079. Their structures were determined with the help of extensive spectroscopic analyses and absolute configuration of compound 1 was rationalized by quantum chemical calculations of the electronic circular dichroism spectra.
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Affiliation(s)
- Zhang-Gui Ding
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, P.R. China
| | - Jian-Hai Ding
- Engineering and Technology Research Center of Liupanshan Resources, College of Chemistry and Chemical Engineering, Ningxia Normal University, Guyuan, P. R. China
| | - Jiang-Yuan Zhao
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, P.R. China
| | - Ming-Gang Li
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, P.R. China
| | - Dong-Bao Hu
- School of Chemical Biology and Environment, Yuxi Normal University, P.R. China
| | | | | | - Fei Wang
- BioBioPha Co., Ltd., Kunming, P.R. China
| | - Meng-Liang Wen
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, P.R. China
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Ding JH, Ding ZG, Zhao JY, Li MG, Hu DB, Jiang XJ, Zhou DS, Wang F, Wen ML. A new pregnane steroid from cultures of Aspergillus versicolor. Nat Prod Res 2018; 33:1885-1890. [DOI: 10.1080/14786419.2018.1478828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jian-Hai Ding
- College of Chemistry and Chemical Engineering, Ningxia Normal University , Guyuan, PR China
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University , Kunming, PR China
| | - Zhang-Gui Ding
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University , Kunming, PR China
| | - Jiang-Yuan Zhao
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University , Kunming, PR China
| | - Ming-Gang Li
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University , Kunming, PR China
| | - Dong-Bao Hu
- School of Chemical Biology and Environment, Yuxi Normal University , Yuxi, PR China
| | | | | | - Fei Wang
- BioBioPha Co., Ltd ., Kunming, PR China
| | - Meng-Liang Wen
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University , Kunming, PR China
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Chunyu WX, Zhao JY, Ding ZG, Wang YX, Han XL, Li MG, Wen ML. A New Dichlorinated Aromatic Lactone from the Tin Mine Tailings-Derived Fungus Torula sp. YIM DT 10072. Chem Nat Compd 2018. [DOI: 10.1007/s10600-018-2372-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Wang RJ, Wen ML, Zhou Q, Wei XW, Li H, Zhao YB, Qi YF, Luan J, Zhou XF. [Downregulation of large conductance calcium-activated potassium channels in paraventricular nucleus contributes to sympathoexcitation in rats with chronic heart failure]. Zhonghua Xin Xue Guan Bing Za Zhi 2018; 46:178-186. [PMID: 29562421 DOI: 10.3760/cma.j.issn.0253-3758.2018.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Objective: To elucidate the association between large conductance calcium-activated potassium channels (BKCa) in the paraventricular hypothalamic nucleus (PVN) and sympathetic outflow in rats with chronic heart failure (CHF) . Methods: Male Wistar rats (6-7 weeks old) were randomized to sham operated group and CHF group (coronary artery ligation) . Two weeks after operation, BKCa inhibitor Iberiotoxin (IBTX) was infused into PVN by osmotic minipumps, rats were divided into following groups: sham+aCSF, CHF+aCSF, sham+low dose IBTX (0.125 nmol/nl) , CHF+low dose IBTX, sham+moderate dose IBTX (1.25 nmol/nl) , CHF+moderate dose IBTX, sham+ high dose IBTX (12.5 nmol/nl) , and CHF+high dose IBTX (n=6 each) . Additional rats were grouped as follows: sham+vehicle, sham+KCNMB4 knockdown (by rAAV2-KCNMB4 shRNA virus injection in PVN) , CHF+vehicle, CHF+ KCNMB4 knockdown group (n=6 each) . The cardiac function was determined by echocardiography, left ventricular hemodynamics were measured invasively, renal sympathetic nerve activity (RSNA) was recorded at 6 weeks after coronary artery ligation or sham operation. The contents of norepinephrine (NE) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) in plasma were determined by enzyme-linked immunosorbent assay. The protein and mRNA expression of KCNMB4 in PVN were measured by immunofluorescence staining, Western blot, and real-time PCR, mRNA expression of BKCa in PVN was detected by real-time PCR. Results: Compared with the sham operation group, the cardiac function of the heart failure group was significantly reduced (P<0.05) , and the plasma NE and the serum NT-proBNP were significantly elevated (P<0.05) . The protein and mRNA expression of KCNMB4 in PVN were obviously down-regulated in CHF rats (P<0.05) . After perfusion of IBTX or KCNMB4 knockdown by microinjection of rAAV2-KCNMB4 shRNA virus,right ventricular weight/body weight and lung weight/body weight ratio as well as left ventricular end-diastolic diameter were increased and left ventricular ejection fraction was decreased (all P<0.05) , the sympathetic driving indexes was increased in sham rats, changes of these parameters further aggravated in CHF rats (P<0.05) . KCNMB4 knockdown further downregulated protein expression in PVN of CHF rats. Conclusion: Downregulation and blunted function of BKCa in PVN may contribute to sympathoexcitation and deterioration of cardiac function in rats with chronic heart failure.
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Affiliation(s)
- R J Wang
- Departments of Biotechnology, College of Life Science, Jilin Normal University, Siping 136000, China
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Chunyu WX, Zhao JY, Ding ZG, Han XL, Wang YX, Ding JH, Wang F, Li MG, Wen ML. A new cyclohexenone from the tin mine tailings-derived fungus Aspergillus flavus YIM DT 10012. Nat Prod Res 2018; 33:113-116. [PMID: 29376405 DOI: 10.1080/14786419.2018.1431636] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new cyclohexenone, named phomaligol D (1), together with two known compounds, kojic acid (2) and phomaligol A (3) were isolated from the tin mine tailings-derived fungus Aspergillus flavus YIM DT 10012. Their structures were elucidated by detailed analysis of spectroscopic data.
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Affiliation(s)
- Wei-Xun Chunyu
- a Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan Institute of Microbiology, Yunnan University , Kunming , PR China.,e Department of Pathogen Biology and Immunology , Kunming Medical University , Kunming , PR China
| | - Jiang-Yuan Zhao
- b Key Laboratory of Medicinal Chemistry for Natural Resource of the Ministry of Education , Yunnan University , Kunming , PR China
| | - Zhang-Gui Ding
- a Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan Institute of Microbiology, Yunnan University , Kunming , PR China
| | - Xiu-Lin Han
- a Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan Institute of Microbiology, Yunnan University , Kunming , PR China
| | - Yong-Xia Wang
- a Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan Institute of Microbiology, Yunnan University , Kunming , PR China
| | - Jian-Hai Ding
- a Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan Institute of Microbiology, Yunnan University , Kunming , PR China.,c Engineering and Technology Research Center of Liupanshan Resources, College of Chemistry and Chemical Engineering , Ningxia Normal University , Guyuan , PR China
| | - Fei Wang
- d BioBioPha Co., Ltd. , Kunming , PR China
| | - Ming-Gang Li
- a Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan Institute of Microbiology, Yunnan University , Kunming , PR China
| | - Meng-Liang Wen
- a Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan Institute of Microbiology, Yunnan University , Kunming , PR China
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Ding ZG, Zhao JY, Ding JH, Chunyu WX, Li MG, Gu SJ, Wang F, Wen ML. A novel phenylspirodrimane dimer from cultures of the fungus Stachybotrys chartarum. Nat Prod Res 2017; 32:2370-2374. [DOI: 10.1080/14786419.2017.1413565] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Zhang-Gui Ding
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
| | - Jiang-Yuan Zhao
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
| | - Jian-Hai Ding
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
- Engineering and Technology Research Center of Liupanshan Resources, College of Chemistry and Chemical Engineering, Ningxia Normal University, Guyuan, PR China
| | - Wei-Xun Chunyu
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
| | - Ming-Gang Li
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
| | | | - Fei Wang
- BioBioPha Co., Ltd., Kunming, PR China
| | - Meng-Liang Wen
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
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Jiang M, Yin M, Wu S, Han X, Ji K, Wen M, Lu T. GdmRIII, a TetR Family Transcriptional Regulator, Controls Geldanamycin and Elaiophylin Biosynthesis in Streptomyces autolyticus CGMCC0516. Sci Rep 2017; 7:4803. [PMID: 28684749 PMCID: PMC5500506 DOI: 10.1038/s41598-017-05073-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 05/24/2017] [Indexed: 11/13/2022] Open
Abstract
Geldanamycin and elaiophylin are co-produced in several Streptomyces strains. However, the regulation of their biosynthesis is not fully understood yet. Herein the function of a TetR family regulator GdmRIII, which is located in the biosynthetic gene cluster of geldanamycin, was studied to understand the regulatory mechanism of geldanamycin biosynthesis in Streptomyces autolyticus CGMCC0516. The production of geldanamycin decreased substantially in a ΔgdmRIII mutant and the yield of three compounds which were thought to be geldanamycin congeners greatly increased. Surprisingly, the structural elucidation of these compounds showed that they were elaiophylin and its analogues, which implied that GdmRIII not only played a positive regulatory role in the biosynthesis of geldanamycin, but also played a negative role in elaiophylin biosynthesis. GdmRIII affected the expression of multiple genes in both gene clusters, and directly regulated the expression of gdmM, gdmN, and elaF by binding to the promoter regions of these three genes. A conserved non-palindromic sequence was found among the binding sites of elaF. Our findings suggested that the biosynthetic pathways of geldanamycin and elaiophylin were connected through GdmRIII, which might provide a way for Streptomyces to coordinate the biosynthesis of these compounds for better adapting to environment changes.
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Affiliation(s)
- MingXing Jiang
- Yunnan Institute of Microbiology, Yunnan University, 2 North Cui Hu Road, Kunming, Yunnan, 650091, China
| | - Min Yin
- Yunnan Institute of Microbiology, Yunnan University, 2 North Cui Hu Road, Kunming, Yunnan, 650091, China
| | - ShaoHua Wu
- Yunnan Institute of Microbiology, Yunnan University, 2 North Cui Hu Road, Kunming, Yunnan, 650091, China
| | - XiuLin Han
- Yunnan Institute of Microbiology, Yunnan University, 2 North Cui Hu Road, Kunming, Yunnan, 650091, China
| | - KaiYan Ji
- Yunnan Institute of Microbiology, Yunnan University, 2 North Cui Hu Road, Kunming, Yunnan, 650091, China
| | - MengLiang Wen
- Yunnan Institute of Microbiology, Yunnan University, 2 North Cui Hu Road, Kunming, Yunnan, 650091, China.
| | - Tao Lu
- Yunnan Institute of Microbiology, Yunnan University, 2 North Cui Hu Road, Kunming, Yunnan, 650091, China.
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Chunyu WX, Ding ZG, Zhao JY, Wang YX, Han XL, Li MG, Wen ML. Two new diketopiperazines from the tin mine tailings-derived fungus Schizophyllum commune YIM DT 10058. Nat Prod Res 2017; 31:1566-1572. [DOI: 10.1080/14786419.2016.1274894] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Wei-Xun Chunyu
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
| | - Zhang-Gui Ding
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
| | - Jiang-Yuan Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource of the Ministry of Education, Yunnan University, Kunming, PR China
| | - Yong-Xia Wang
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
| | - Xiu-Lin Han
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
| | - Ming-Gang Li
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
| | - Meng-Liang Wen
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, PR China
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17
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Affiliation(s)
- Can-Can Zhang
- School of Pharmaceutical Sciences, Chinese Center for Chirality, Hebei University, Baoding, China
| | - Shuang-Shuang Ding
- School of Pharmaceutical Sciences, Chinese Center for Chirality, Hebei University, Baoding, China
| | - Wen-Si Shi
- School of Pharmaceutical Sciences, Chinese Center for Chirality, Hebei University, Baoding, China
| | - Fei Cao
- School of Pharmaceutical Sciences, Chinese Center for Chirality, Hebei University, Baoding, China
| | - Hua-Jie Zhu
- School of Pharmaceutical Sciences, Chinese Center for Chirality, Hebei University, Baoding, China
| | - Meng-Liang Wen
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan University, Kunming, China
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Chunyu WX, Ding ZG, Li MG, Zhao JY, Gu SJ, Gao Y, Wang F, Ding JH, Wen ML. Stachartins A - E, Phenylspirodrimanes from the Tin Mine Tailings-Associated FungusStachybotrys chartarum. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201600020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wei-Xun Chunyu
- Key Laboratory for Microbial Resources; Ministry of Education; Yunnan Institute of Microbiology; Yunnan University; Kunming 650091 P. R. China
| | - Zhang-Gui Ding
- Key Laboratory for Microbial Resources; Ministry of Education; Yunnan Institute of Microbiology; Yunnan University; Kunming 650091 P. R. China
| | - Ming-Gang Li
- Key Laboratory for Microbial Resources; Ministry of Education; Yunnan Institute of Microbiology; Yunnan University; Kunming 650091 P. R. China
| | - Jiang-Yuan Zhao
- Key Laboratory for Microbial Resources; Ministry of Education; Yunnan Institute of Microbiology; Yunnan University; Kunming 650091 P. R. China
| | - Shao-Jie Gu
- BioBioPha Co., Ltd.; Kunming 650201 P. R. China
| | - Yuan Gao
- BioBioPha Co., Ltd.; Kunming 650201 P. R. China
| | - Fei Wang
- BioBioPha Co., Ltd.; Kunming 650201 P. R. China
| | - Jian-Hai Ding
- College of Chemistry and Chemical Engineering; Ningxia Normal University; Guyuan 756000 P. R. China
| | - Meng-Liang Wen
- Key Laboratory for Microbial Resources; Ministry of Education; Yunnan Institute of Microbiology; Yunnan University; Kunming 650091 P. R. China
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Zhu HJ, Li WX, Hu DB, Wen ML. Discussion of absolute configuration for bioactive Griseusins by comparing computed optical rotations and electronic circular dichroism with the experimental results. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.09.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wang YX, Li YP, Liu JH, Xiao W, Lai YH, Li ZY, Ding ZG, Wen ML, Cui XL. Gracilimonas mengyeensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-western China. Int J Syst Evol Microbiol 2013; 63:3989-3993. [PMID: 23710054 DOI: 10.1099/ijs.0.052043-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, Gram-staining-negative, pale red-pigmented, non-motile, rod-shaped, moderately halophilic bacterium, designated strain YIM J14(T), was isolated from a sediment sample from a salt mine in Yunnan, south-western China. Growth occurred at NaCl concentrations of between 2 % and 15 % (w/v) and optimally with 5-9 % NaCl. The optimum temperature and pH for growth of the strain were 28 °C and pH 7.5. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c/10-methyl-C16 : 0. The polar lipid profile was composed predominantly of diphosphatidylglycerol, phosphatidylcholine and one unknown phospholipid. Minor amounts of other lipids were also detectable. The genomic DNA G+C content was 47.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain YIM J14(T) was related to Gracilimonas tropica in the phylum Bacteroidetes. The level of 16S rRNA gene sequence similarity between strain YIM J14(T) and Gracilimonas tropica CL-CB462(T) was 96.9 %. A DNA-DNA hybridization experiment between strain YIM J14(T) and Gracilimonas tropica indicated levels of relatedness of 28 %. Chemotaxonomic data supported the placement of strain YIM J14(T) in the genus Gracilimonas. DNA-DNA hybridization and biochemical and physiological characterization allowed strain YIM J14(T) to be differentiated from Gracilimonas tropica. It is therefore considered to represent a novel species of the genus Gracilimonas, for which the name Gracilimonas mengyeensis sp. nov. is proposed. The type strain YIM J14(T) ( = ACCC 10717(T) = DSM 21985(T)).
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Affiliation(s)
- Yong-Xia Wang
- Key Laboratory for Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Ya-Ping Li
- Key Laboratory for Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Ji-Hui Liu
- Technology Research Center, HongyunHonghe Tobacco (Group), Kunming, Yunnan 650202, P. R. China
- Key Laboratory for Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Wei Xiao
- Key Laboratory for Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Yong-Hong Lai
- Key Laboratory for Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Zhi-Ying Li
- Key Laboratory for Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Zhang-Gui Ding
- Key Laboratory for Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Meng-Liang Wen
- Key Laboratory for Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Xiao-Long Cui
- Key Laboratory for Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
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Li QM, Ren J, Zhou BD, Bai B, Liu XC, Wen ML, Zhu HJ. Determining the absolute configuration of benzopyrenomycin by optical rotation, electronic circular dichroism, and population analysis of different conformations via DFT methods and experiments. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.01.082] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Xiao W, Wang ZG, Wang YX, Schneegurt MA, Li ZY, Lai YH, Zhang SY, Wen ML, Cui XL. Comparative molecular analysis of the prokaryotic diversity of two salt mine soils in southwest China. J Basic Microbiol 2013; 53:942-52. [PMID: 23457089 DOI: 10.1002/jobm.201200200] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 08/25/2012] [Indexed: 11/09/2022]
Abstract
While much is known about the microbial diversity in some hypersaline environments, little is known about those of salt mine tunnel soils. The objective of this study was to conduct a comprehensive phylogenetic comparison of the archaeal and bacterial communities present in Yipinglang salt mine (YPL) and Qiaohou salt mine (QH) tunnels differing in salinity and salt composition using 16S rRNA gene clone libraries. Two hundred twenty-eight sequences for QH and 182 sequences for YPL were analyzed by amplified ribosomal DNA-restriction analysis. Libraries revealed 44 bacterial and 57 archaeal different operational taxonomic units belonging to at least 8 bacterial and 3 archaeal divisions, but not all divisions were observed in both salt mines. The bacterial community affiliated with the Bacteroidetes was the most abundant (60% of clones) in QH, while the community in YPL was dominated by δ-Proteobacteria (45% of clones). All archaeal clones from QH were affiliated with Halobacteriaceae. In contrast, in the YPL library, 49% of clones belonged to Halobacteriaceae, 31% of clones related to unclassified archaea, and 21% of clones belonged to Crenarchaeota. Bioinformatic analysis and comparisons showed that the clone libraries were significantly different between two salt mines.
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Affiliation(s)
- Wei Xiao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, P.R. China
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Wang YX, Liu JH, Xiao W, Ma XL, Lai YH, Li ZY, Ji KY, Wen ML, Cui XL. Aliifodinibius roseus gen. nov., sp. nov., and Aliifodinibius sediminis sp. nov., two moderately halophilic bacteria isolated from salt mine samples. Int J Syst Evol Microbiol 2013; 63:2907-2913. [PMID: 23334882 DOI: 10.1099/ijs.0.043869-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two rod-shaped, non-motile bacteria were isolated from two separate salt mines in Yunnan, south-western China. These strains, designated YIM D15(T) and YIM J21(T), were Gram-negative and moderately halophilic. The two strains required 6-10 % NaCl (w/v; optimal) for growth. The DNA G+C contents of strains YIM D15(T) and YIM J21(T) were 49.0 mol% and 48.4 mol%, respectively. The predominant isoprenoid quinone was MK-7. The polar lipid profiles of strains YIM D15(T) and YIM J21(T) were composed predominantly of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, three unknown polar lipids and one glycolipid. Minor amounts of other lipids were also detectable. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c/10 methyl-C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct clade with the genus Fodinibius (in the phylum Bacteroidetes) and were related to the species Fodinibius salinus, with sequence similarities of 91.9-92.4 %. Analyses of 16S rRNA gene sequences revealed that strains YIM D15(T) and YIM J21(T) were related to each other (97.3 % sequence similarity). The DNA-DNA hybridization relatedness between the two isolates was 34 %. On the basis of the phylogenetic analysis, DNA-DNA hybridization relatedness, phenotypic and chemotaxonomic characteristics, strains YIM D15(T) and YIM J21(T) should be classified as members of a novel genus and as two novel species, for which the names Aliifodinibius roseus gen. nov., sp. nov. (type strain YIM D15(T) = ACCC 10715(T) = KCTC 23442(T)) and Aliifodinibius sediminis sp. nov. (type strain YIM J21(T) = ACCC 10714(T) = DSM 21194(T)) are proposed.
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Affiliation(s)
- Yong-Xia Wang
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Ji-Hui Liu
- The Technology Research Center, HongyunHonghe Tobacco (Group), Co., Ltd, Kunming, Yunnan 650202, PR China.,The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Wei Xiao
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Liang Ma
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Hong Lai
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Zhi-Ying Li
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Kai-Yan Ji
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Meng-Liang Wen
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Long Cui
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Ding ZG, Zhao JY, Li MG, Huang R, Li QM, Cui XL, Zhu HJ, Wen ML. Griseusins F and G, spiro-naphthoquinones from a tin mine tailings-derived alkalophilic Nocardiopsis species. J Nat Prod 2012; 75:1994-1998. [PMID: 23095059 DOI: 10.1021/np3004936] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Griseusins F (1) and G (2), two 2a-hydro-8a-(2-oxopropyl)-substituted spiro-naphthoquinones with a previously undescribed C23 polyketide skeleton, were isolated from a Yunnan tin mine tailings-derived alkalophilic actinomycete, Nocardiopsis sp. YIM DT266. Their complete structure assignments with the absolute stereochemistry were elucidated by spectroscopic data, X-ray crystal diffraction, calculation of optical rotation, and CD spectroscopic analysis. Compounds 1 and 2 exhibited strong cytotoxicity (IC50 0.37-0.82 μM) and antibacterial activity (MIC 0.80-1.65 μg/mL) against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) in vitro.
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Affiliation(s)
- Zhang-Gui Ding
- Key Laboratory for Microbial Resources, Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University , Kunming, 650091, People's Republic of China
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Wang YX, Liu JH, Xiao W, Zhang XX, Li YQ, Lai YH, Ji KY, Wen ML, Cui XL. Fodinibius salinus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a salt mine. Int J Syst Evol Microbiol 2011; 62:390-396. [PMID: 21441370 DOI: 10.1099/ijs.0.025502-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, moderately halophilic, rod-shaped bacterium, designated strain YIM D17(T), was isolated from a sample of sediment from a salt mine in Yunnan, south-western China. The taxonomy of strain YIM D17(T) was investigated using a polyphasic approach. Strain YIM D17(T) was Gram-stain-negative, strictly aerobic and non-motile and formed pink colonies on marine agar. Optimal growth occurred at 37 °C, pH 7.5-8.0 and in the presence of 10-15 % (w/v) NaCl. The major menaquinone was MK-7. The polar lipid profile was composed predominantly of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, one phospholipid, one glycolipid and one aminolipid. Minor amounts of other lipids were also detectable. The predominant cellular fatty acids were iso-C(17 : 1)ω9c/10-methyl-C(16 : 0) (24.0 %), iso-C(15 : 0) (23.6 %) and C(16 : 1)ω7c/C(16 : 1)ω6c (13.8 %). The DNA G+C content was 43.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct clade with the genera Gracilimonas and Balneola (both in the phylum Bacteroidetes) and was related to the species Gracilimonas tropica, Balneola vulgaris and Balneola alkaliphila, with sequence similarities of 85.6 %, 83.0 % and 82.8 % to the respective type strains. On the basis of its phenotypic, chemotaxonomic and phylogenetic features, strain YIM D17(T) represents a novel species of a new genus, for which the name Fodinibius salinus gen. nov., sp. nov. is proposed. The type strain is YIM D17(T) ( = ACCC 10716(T) = DSM 21935(T)).
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Affiliation(s)
- Yong-Xia Wang
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Ji-Hui Liu
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Wei Xiao
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100080, PR China
| | - Yi-Qing Li
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Hong Lai
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Kai-Yan Ji
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Meng-Liang Wen
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Long Cui
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Ding ZG, Li MG, Ren J, Zhao JY, Huang R, Wang QZ, Cui XL, Zhu HJ, Wen ML. Phenazinolins A–E: novel diphenazines from a tin mine tailings-derived Streptomyces species. Org Biomol Chem 2011; 9:2771-6. [DOI: 10.1039/c1ob05044c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tian SP, Wang YX, Hu B, Zhang XX, Xiao W, Chen Y, Lai YH, Wen ML, Cui XL. Litoribacter ruber gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a soda lake sediment. Int J Syst Evol Microbiol 2010; 60:2996-3001. [DOI: 10.1099/ijs.0.021626-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel alkaliphilic, halotolerant, rod-shaped bacterium, designated strain YIM CH208T, was isolated from a soda lake in Yunnan, south-west China. The taxonomy of strain YIM CH208T was investigated by a polyphasic approach. Strain YIM CH208T was Gram-negative, strictly aerobic and non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.5 and 0.5–2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genus Echinicola in the phylum Bacteroidetes and was related to the species Echinicola pacifica and Rhodonellum psychrophilum, with sequence similarity of 91.7 and 91.6 % to the respective type strains. The DNA G+C content was 45.1 mol%. The major respiratory quinone was menaquinone-7 (MK-7). The predominant cellular fatty acids were iso-C17 : 1
ω9c (19.9 %), C15 : 0 3-OH (12.1 %), iso-C17 : 0 3-OH (11.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c; 10.7 %) and C17 : 1
ω6c (8.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain YIM CH208T represents a novel species of a new genus, for which the name Litoribacter ruber gen. nov., sp. nov. is proposed. The type strain of Litoribacter ruber is YIM CH208T (=ACCC 05414T =KCTC 22899T).
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Affiliation(s)
- Shi-Ping Tian
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Xia Wang
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Bin Hu
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100080, PR China
| | - Wei Xiao
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yun Chen
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Hong Lai
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Meng-Liang Wen
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Long Cui
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Ding ZG, Li MG, Zhao JY, Ren J, Huang R, Xie MJ, Cui XL, Zhu HJ, Wen ML. Naphthospironone A: An Unprecedented and Highly Functionalized Polycyclic Metabolite from an Alkaline Mine Waste Extremophile. Chemistry 2010; 16:3902-5. [DOI: 10.1002/chem.200903198] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Liu JH, Wang YX, Zhang XX, Wang ZG, Chen YG, Wen ML, Xu LH, Peng Q, Cui XL. Salinarimonas rosea gen. nov., sp. nov., a new member of the α-2 subgroup of the Proteobacteria. Int J Syst Evol Microbiol 2010; 60:55-60. [DOI: 10.1099/ijs.0.006981-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped, facultatively anaerobic, halotolerant bacterial strain, designated YIM YD3T, was isolated from a salt mine in Yunnan, south-west China. The taxonomy of strain YIM YD3T was investigated by a polyphasic approach. Strain YIM YD3T was motile, formed pink colonies and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and two unknown phospholipids. The major fatty acids (>10 % of total fatty acids) were C18 : 1
ω7c, C18 : 1
ω9c, C16 : 0 and C19 : 0 cyclo ω8c. The DNA G+C content was 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genera Balneimonas, Bosea, Chelatococcus and Microvirga in the order Rhizobiales, with highest levels of 16S RNA gene sequence similarity to the type strain of Balneimonas flocculans (93.5 %). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YIM YD3T represents a novel species in a new genus, for which the name Salinarimonas rosea gen. nov., sp. nov. is proposed, with strain YIM YD3T (=KCTC 22346T=CCTCC AA208038T) as the type strain.
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Affiliation(s)
- Ji-Hui Liu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Xia Wang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100080, PR China
| | - Zhi-Gang Wang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yi-Guang Chen
- College of Bio-resources and Environmental Science, Jishou University, Jishou, Hunan 416000, PR China
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Meng-Liang Wen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Li-Hua Xu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Qian Peng
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Long Cui
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Chen YG, Cui XL, Wang YX, Zhang YQ, Tang SK, Li WJ, Liu ZX, Wen ML, Peng Q. Virgibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China. Int J Syst Evol Microbiol 2009; 59:2058-63. [PMID: 19605714 DOI: 10.1099/ijs.0.003624-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, moderately halophilic, alkalitolerant, strictly aerobic, oxidase- and catalase-positive, rod-shaped bacterium, strain YIM kkny3T, was isolated from a sediment sample collected from a salt lake in the Qaidam Basin of north-west China. Cells were motile by means of peritrichous flagella and formed ellipsoidal endospores lying in subterminal swollen sporangia. Growth occurred with 1-20% (w/v) total salts (optimum, 5-10%) and at pH 6.0-10.5 (optimum, pH 7.5-8.0) and 10-55 degrees C (optimum, 35-40 degrees C). It was unable to grow with NaCl as the only salt. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The strain contained menaquinone 7 (MK-7) as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as polar lipids. The major cellular fatty acids were anteiso-C15:0 and anteiso-C17:0. The DNA G+C content was 40.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM kkny3T belonged to the genus Virgibacillus, and was most closely related to the type strains of Virgibacillus olivae (97.1% similarity), Virgibacillus marismortui (97.0%) and Virgibacillus kekensis (96.8%). Levels of DNA-DNA relatedness between strain YIM kkny3T and the type strains of V. olivae, V. marismortui and V. kekensis were 12.4, 10.6 and 15.7%, respectively. The combination of phylogenetic analysis, genotypic data, phenotypic characteristics and chemotaxonomic differences indicated that strain YIM kkny3T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus sediminis sp. nov. is proposed. The type strain is YIM kkny3T (=CCTCC AA 207023T=DSM 19797T=KCTC 13193T).
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Affiliation(s)
- Yi-Guang Chen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Wang ZG, Wang YX, Liu JH, Chen YG, Zhang XX, Wen ML, Xu LH, Peng Q, Cui XL. Fodinibacter luteus gen. nov., sp. nov., an actinobacterium isolated from a salt mine. Int J Syst Evol Microbiol 2009; 59:2185-90. [PMID: 19605729 DOI: 10.1099/ijs.0.006882-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive-staining, aerobic, catalase- and oxidase-positive, irregular short rod-shaped actinobacterium, designated strain YIM C003T, was isolated from a salt mine in Yunnan, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM C003T was most closely related to strains of the genera Knoellia (94.2-96.0% similarity), Oryzihumus (95.6%), Terrabacter (94.9-95.4%), Janibacter (94.9-95.4%), Kribbia (95.0%), Lapillicoccus (95.0%) and Phycicoccus (94.2-95.0%) of the family Intrasporangiaceae and that it formed an independent monophyletic lineage with three strains of Oryzihumus leptocrescens. The DNA G+C content of strain YIM C003T was 72.0 mol%. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Mycolic acids were not detected. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The major cellular fatty acids were C18:1omega9c and C16:0. These chemotaxonomic properties, together with data from phylogenetic analysis, enabled the novel isolate to be differentiated from all other members of the family. A novel species in a new genus, Fodinibacter luteus gen. nov., sp. nov., is proposed, with strain YIM C003T (=DSM 21208T=CCTCC AA 208036T) as the type strain of Fodinibacter luteus.
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Affiliation(s)
- Zhi-Gang Wang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Wang YX, Wang ZG, Liu JH, Chen YG, Zhang XX, Wen ML, Xu LH, Peng Q, Cui XL. Sediminimonas qiaohouensis gen. nov., sp. nov., a member of the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol 2009; 59:1561-7. [PMID: 19528203 DOI: 10.1099/ijs.0.006965-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two aerobic bacterial strains, YIM B024(T) and YIM B025, were isolated from a salt mine in Yunnan, south-west China. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. The novel strains grew at 15-37 degrees C, pH 6.5-9.0 and 0.25-20 % (w/v) NaCl; optimum growth was observed at 28-30 degrees C, pH 7.0-8.5 and 1.5-10 % NaCl. Oxidase, catalase and nitrate-reducing activities were detected. The two strains were closely related to each other with a 16S rRNA gene sequence similarity of 100 %. DNA-DNA hybridization experiments revealed high relatedness values (90+/-0.4 %) between strains YIM B024(T) and YIM B025, which suggested that these two new strains constituted a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a loose cluster with members of the genus Roseivivax in the Roseobacter clade, but were clearly separated from this genus. The levels of 16S rRNA gene sequence similarity between the two isolates and members of the genus Roseivivax ranged from 92.4 to 93.9 %. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and four unknown phospholipids. The major cellular fatty acids were C(18 : 1)omega7c, C(16 : 0), C(18 : 1)omega9c, 11-methyl C(18 : 1)omega7c and C(19 : 0) cyclo omega8c. The sole respiratory quinone was Q-10 and the genomic DNA G+C content was 63.0-64.1 mol%. The distinct phylogenetic position and a combination of phenotypic and chemotaxonomic characteristics supported the proposal of the new isolates as representing a novel species in a new genus, for which the name Sediminimonas qiaohouensis gen. nov., sp. nov. is proposed. The type strain of the type species is YIM B024(T) (=KCTC 22349(T)=CCTCC AA 208033(T)).
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Affiliation(s)
- Yong-Xia Wang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Chen YG, Cui XL, Li QY, Wang YX, Tang SK, Liu ZX, Wen ML, Peng Q, Xu LH. Saccharospirillum salsuginis sp. nov., a gammaproteobacterium from a subterranean brine. Int J Syst Evol Microbiol 2009; 59:1382-6. [PMID: 19502320 DOI: 10.1099/ijs.0.003616-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yi-Guang Chen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Chen YG, Cui XL, Wang YX, Zhang YQ, Li QY, Liu ZX, Wen ML, Peng Q, Li WJ. Salinicoccus albus sp. nov., a halophilic bacterium from a salt mine. Int J Syst Evol Microbiol 2009; 59:874-9. [PMID: 19329623 DOI: 10.1099/ijs.0.003251-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-positive-staining, catalase- and oxidase-positive, non-motile, non-spore-forming coccus, designated YIM-Y21(T), was isolated from a salt mine in Yunnan, south-west China. The strain was moderately halophilic, facultatively alkaliphilic and obligately aerobic. Colonies were white. Growth occurred with 1.0-30.0 % NaCl (optimum, 10.0 % NaCl), at pH 6.0-10.0 (optimum, pH 8.5) and at 5-40 degrees C (optimum, 25 degrees C). The major amino acid constituents of the cell wall were glycine and lysine. The major cellular fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(15 : 0). MK-6 was the predominant respiratory quinone, with MK-7 present in minor amounts. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The DNA G+C content was 46.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain YIM-Y21(T) was most closely related to the type strains of the nine recognized species of the genus Salinicoccus. The sequence similarities between the isolate and the type strains of members of this genus were in the range of 90.6-93.8 %, which indicated that strain YIM-Y21(T) is a representative of a novel species within the genus Salinicoccus. Together with the phenotypic characteristics and chemotaxonomic differences, these results support the proposal of a novel species of the genus Salinicoccus, Salinicoccus albus sp. nov., with YIM-Y21(T) (=CCTCC AA 207024(T) =DSM 19776(T) =KCTC 13192(T)) as the type strain.
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Affiliation(s)
- Yi-Guang Chen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Ding ZG, Zhao JY, Yang PW, Li MG, Huang R, Cui XL, Wen ML. (1)H and (13)C NMR assignments of eight nitrogen containing compounds from Nocardia alba sp.nov (YIM 30243(T)). Magn Reson Chem 2009; 47:366-370. [PMID: 19165845 DOI: 10.1002/mrc.2393] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An unprecedented new natural product named nocarsin A (1), 5H-4a,6,7a-triazacyclopenta[cd]indene-5,7(6H)-dione (1), together with seven known compounds lumichrome (2), cyclo (L-Leu-L-Tyr) (3), cyclo (L-Ala-L-Ile) (4), cyclo (L-Ala-L-Leu) (5), cyclo (L-Val-L-Ala) (6), 5-methyluracil (7) and uracil (8), was isolated from Nocardia alba sp.nov (YIM 30243(T)), which was isolated from a soil sample collected from Yunnan Province, P. R. China. NMR techniques including COSY, HSQC, ROESY, and HMBC were used to elucidate the structures of these compounds. We report the unambiguous assignments of the (1)H and (13)C NMR spectra of the new compound nocarsin A (1).
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Affiliation(s)
- Zhang-Gui Ding
- Key Laboratory for Microbial Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Huang HY, Chen YG, Wang YX, Liu JH, Tang SK, Peng Q, Wen ML, Yu H, Cui XL. Halomonas sediminis sp. nov., a new halophilic bacterium isolated from salt-lake sediment in China. Extremophiles 2008; 12:829-35. [DOI: 10.1007/s00792-008-0189-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2008] [Accepted: 09/01/2008] [Indexed: 11/29/2022]
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Chen YG, Cui XL, Zhang YQ, Li WJ, Wang YX, Xu LH, Peng Q, Wen ML, Jiang CL. Gracilibacillus quinghaiensis sp. nov., isolated from salt-lake sediment in the Qaidam Basin, north-west China. Syst Appl Microbiol 2008; 31:183-9. [DOI: 10.1016/j.syapm.2008.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Chen YG, Cui XL, Fritze D, Chai LH, Schumann P, Wen ML, Wang YX, Xu LH, Jiang CL. Virgibacillus kekensis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China. Int J Syst Evol Microbiol 2008; 58:647-53. [PMID: 18319472 DOI: 10.1099/ijs.0.65365-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, moderately halophilic, motile, strictly aerobic, endospore-forming, oxidase- and catalase-positive, rod-shaped bacterium, strain YIM kkny16(T), was isolated from a saline mud sample collected from the Keke salt lake in the Qaidam Basin, north-west China. This isolate grew in the presence of 0-25 % (w/v) NaCl and at pH 6.0-10.0 and 10-50 degrees C; optimum growth was observed with 10 % (w/v) NaCl and at pH 7.0 and 37 degrees C. Strain YIM kkny16(T) had meso-diaminopimelic acid as the diagnostic diamino acid, MK-7 as the predominant respiratory quinone, with a significant amount of MK-6, and anteiso-C(15 : 0), iso-C(14 : 0) and C(16 : 1)omega7c alcohol as major fatty acids. Major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 41.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain YIM kkny16(T) was a member of the genus Virgibacillus, exhibiting sequence similarities of 94.9-97.3 % to the type strains of recognized Virgibacillus species. Strain YIM kkny16(T) could be differentiated from recognized Virgibacillus species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. On the basis of evidence from this polyphasic study, strain YIM kkny16(T) is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus kekensis sp. nov. is proposed. The type strain is YIM kkny16(T) (=DSM 17056(T)=CGMCC 1.6298(T)).
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Affiliation(s)
- Yi-Guang Chen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Chen YG, Cui XL, Kroppenstedt RM, Stackebrandt E, Wen ML, Xu LH, Jiang CL. Nocardiopsis quinghaiensis sp. nov., isolated from saline soil in China. Int J Syst Evol Microbiol 2008; 58:699-705. [PMID: 18319481 DOI: 10.1099/ijs.0.65441-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A previously unknown Gram-positive, obligately aerobic actinomycete, YIM 28A4(T), was isolated from a sample of saline soil collected from the Qaidam Basin in Qinghai Province, north-west China, and was investigated using a polyphasic taxonomic approach. The strain grew well on most of the media tested, producing white to pale-yellow substrate mycelium, white aerial mycelium and straight to flexuous hyphae. The substrate mycelium was well developed and fragmented with age; the aerial mycelium produced long, straight spore chains. The spore chains were composed of non-motile, smooth-surfaced, rod-shaped spores. No diffusible pigments were produced on any of the media tested. The strain grew in the presence of 0-10 % (w/v) NaCl and at pH 6.0-8.0, with optimum growth occurring at 3 % (w/v) NaCl and pH 7.0. It grew at 10-37 degrees C, the optimum growth temperature being 28 degrees C. Whole-cell hydrolysates of strain YIM 28A4(T) contained meso-diaminopimelic acid and no diagnostic sugars. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The predominant menaquinones were MK-10, MK-10(H(2)), MK-11 and MK-11(H(2)). The major cellular fatty acids were iso-C(16 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 67.1 mol%. The morphological and chemotaxonomic characteristics of the isolate matched those described for Nocardiopsis species. A phylogenetic analysis based on 16S rRNA gene sequence comparisons confirmed that strain YIM 28A4(T) was a member of the genus Nocardiopsis and most closely related to the type strains Nocardiopsis aegyptia DSM 44442(T) and Nocardiopsis halotolerans DSM 44410(T), showing 98.1 and 97.8 % 16S rRNA gene sequence similarity, respectively. Strain YIM 28A4(T) can be differentiated from these type strains by using phenotypic, phylogenetic and DNA-DNA hybridization data. On the basis of the polyphasic evidence, strain YIM 28A4(T) represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis quinghaiensis sp. nov. is proposed. The type strain is YIM 28A4(T) (=DSM 44739(T) =CGMCC 4.3494(T)).
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Affiliation(s)
- Yi-Guang Chen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
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Chen YG, Cui XL, Pukall R, Li HM, Yang YL, Xu LH, Wen ML, Peng Q, Jiang CL. Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China. Int J Syst Evol Microbiol 2008; 57:2327-2332. [PMID: 17911305 DOI: 10.1099/ijs.0.64783-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel yellow-pigmented, non-motile, non-sporulating, catalase- and oxidase-positive, obligately aerobic, moderately halophilic, facultatively alkaliphilic Gram-positive coccus, strain YIM Y15(T), was isolated from a brine sample from a salt mine in Yunnan, south-west China. Strain YIM Y15(T) grew in the presence of 0.5-25 % (w/v) NaCl and at pH 6.0-10.0, with optimum growth at 8-10 % (w/v) NaCl and pH 8.0. It grew at 4-45 degrees C, with optimum growth at 37.0 degrees C. The major cellular fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). Menaquinone 6 (MK-6) was the major respiratory quinone. The cell wall contained Lys and Gly. The DNA G+C content was 46.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that strain YIM Y15(T) was a member of the genus Salinicoccus, with low 16S rRNA gene sequence similarity to the type strains of the five described species of the genus, Salinicoccus alkaliphilus JCM 11311(T) (sequence similarity 96.0 %), Salinicoccus roseus DSM 5351(T) (94.9 %), Salinicoccus jeotgali KCTC 13030(T) (94.8 %), Salinicoccus salsiraiae LMG 22840(T) (94.8 %) and Salinicoccus hispanicus DSM 5352(T) (94.7 %). Together with the phenotypic differences, these results supported the proposal of a novel species of the genus Salinicoccus, Salinicoccus kunmingensis sp. nov., with YIM Y15(T) (=DSM 17847(T) =CGMCC 1.6302(T)) as the type strain.
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MESH Headings
- Aerobiosis/physiology
- Bacterial Typing Techniques
- Base Composition
- Catalase/metabolism
- Cell Wall/chemistry
- China
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Glycine/analysis
- Hydrogen-Ion Concentration
- Locomotion/physiology
- Lysine/analysis
- Molecular Sequence Data
- Oxidoreductases/metabolism
- Phylogeny
- Pigments, Biological/biosynthesis
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Soil Microbiology
- Staphylococcaceae/classification
- Staphylococcaceae/genetics
- Staphylococcaceae/isolation & purification
- Staphylococcaceae/physiology
- Temperature
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Affiliation(s)
- Yi-Guang Chen
- College of Bio-resources and Environmental Science, Jishou University, Jishou, Hunan 416000, PR China
- Yunnan Institute of Microbiology and Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Long Cui
- Yunnan Institute of Microbiology and Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Rüdiger Pukall
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7b, D-38124 Braunschweig, Germany
| | - Hui-Ming Li
- Yunnan Institute of Microbiology and Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Ya-Ling Yang
- Yunnan Salt & Chemical Industry Co., Ltd, Kunming, Yunnan 650091, PR China
| | - Li-Hua Xu
- Yunnan Institute of Microbiology and Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Meng-Liang Wen
- Yunnan Institute of Microbiology and Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Qian Peng
- Yunnan Institute of Microbiology and Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Cheng-Lin Jiang
- Yunnan Institute of Microbiology and Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, Yunnan 650091, PR China
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Chen YG, Cui XL, Li WJ, Xu LH, Wen ML, Peng Q, Jiang CL. Salinicoccus salitudinis sp. nov., a new moderately halophilic bacterium isolated from a saline soil sample. Extremophiles 2007; 12:197-203. [PMID: 18060347 DOI: 10.1007/s00792-007-0116-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Accepted: 09/19/2007] [Indexed: 11/27/2022]
Abstract
A novel pale-yellow-pigmented, moderately halophilic, facultatively alkaliphilic, non-motile, non-spore-forming, catalase- and oxidase-positive, obligately aerobic Gram-positive coccus, strain YIM-C678T was isolated from a saline soil sample collected from a hypersaline habitat in the Qaidam basin, northwest China. The organism grew at 4-37 degrees C and pH 6.0-11.0, with optimum growth at 25 degrees C and pH 8.0. Strain YIM-C678T grew optimally in the presence of 10-12% (w/v) NaCl and growth was observed in 1-25% (w/v) NaCl. The cell wall murein type was L: -Lys-Gly5. Major cellular fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C16:0. Menaquinone 6 (MK-6) was the major respiratory quinone. The DNA G + C content was 46.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain YIM-C678T belonged to the family Staphylococcaceae and was most closely related to the eight described species of the genus Salinicoccus with sequence similarities from 92.2 (S. luteus YIM 70202T) to 97.5% (S. kunmingensis YIM Y15T). The DNA-DNA relatedness between strain YIM-C678T and S. kunmingensis YIM Y15T was 35.4%. Chemotaxonomic data and 16S rRNA gene sequence analysis supported the affiliation of strain YIM-C678T with the genus Salinicoccus. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic differences and DNA-DNA hybridization data supported the view that the bacterium represents a novel species of the genus Salinicoccus, for which the name Salinicoccus salitudinis sp. nov. is proposed, with YIM-C678T (=DSM 17846 = CGMCC 1.6299) as the type strain.
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Affiliation(s)
- Yi-Guang Chen
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, Yunnan 650091, People's Republic of China
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Jiang Y, Li WJ, Xu P, Li MG, Wen ML, Du GH, Xu LH, Jiang CL. Streptomyces roseoalbus sp. nov., an actinomycete isolated from soil in Yunnan, China. Antonie Van Leeuwenhoek 2005; 87:215-20. [PMID: 15803384 DOI: 10.1007/s10482-004-3210-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2004] [Accepted: 09/03/2004] [Indexed: 11/25/2022]
Abstract
A strain YIM 33098T (= CCTCC AA001027T = DSM 41831T) was isolated from a forest soil sample collected from Nanning in Guangxi Province, China, in the course of screening for producers of new drug lead compounds. This strain was identified by using a polyphasic approach. The results showed that it should be assigned to the genus Streptomyces. An almost complete 16S rRNA gene sequence of the strain was determined and compared with those of representative Streptomyces species. Strain YIM 33098T was clustered in the same subclade with Streptomyces tendae ATCC19812T and Streptomyces eurythermus ATCC14975T. Similarities of strain YIM 33098T with the two strains were 97.35% and 97.42%, respectively. Based on the phenotypic and genotypic evidence, it is therefore proposed that strain YIM 33098T should be classified in the genus Streptomyces as a new species under the name of Streptomyces nanningensis sp. nov.
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Affiliation(s)
- Yi Jiang
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Peng LJ, Wen ML, Yao Y. Fentanyl-selective polymeric membrane electrode. Pharmazie 2001; 56:780-2. [PMID: 11683122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
A poly (vinyl chloride) membrane electrode with dibutyl phthalate as plasticizer based on a fentanyl-tetrakis(4-chlorophenyl)borate ion-pair complex for the determination of fentanyl citrate in injections is described. A linear response over the range 1 x 10(-5) mol.dm-3 to 1 x 10(-2) mol.dm-3 drug with a slope of 59.3 +/- 0.6 mV/decade was established. The optimum pH range was 1 to 6. The lower detection limit was 8 x 10(-6) mol.dm-3 fentanyl citrate (2.7 micrograms cm-3 fentanyl). There were negligible interferences from a number of inorganic cations, structural analogues, and some common drug additives used in injections. The electrode proposed has been successfully applied to determine fentanyl citrate in injections. The results correlated well with those obtained by the United States Pharmacopoeia standard procedure.
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Affiliation(s)
- L J Peng
- Department of Chemistry, Yunnan University, Kunming, Yunnan, PR China
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Abstract
The construction and performance characteristics of an ion-selective electrode for fentanyl-drug cation, based on an ion-pair complex with tetrakis[3,5-bis-(trifluoromethyl)phenyl]borate anion in a PVC matrix were studied. A linear response for 1 x 10(-5) mol dm-3 to 1 x 10(-2) mol dm-3 drug with a slope of 57.9 +/- 0.5 mV/decade was established. The optimum pH range was 2 to 6. The lower detection limit was 6.29 x 10(-6) mol dm-3 fentanyl citrate (2.1165 micrograms cm-3 fentanyl). There were negligible interferences from a number of inorganic cations, structural analogues, and some common drug additives in injections. The electrode proposed has been successfully applied to determine fentanyl citrate in injections. The results correlated well with those obtained by the United States Pharmacopoeia standard procedure.
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Affiliation(s)
- L J Peng
- Department of Chemistry, Yunnan University, Kunming, Yunnan 650091, PR China
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Liu ZH, Wen ML, Yao Y, Xiong J. Plastic membrane electrode for the potentiometric determination of pethidine hydrochloride in pharmaceutical preparations. Fresenius J Anal Chem 2000; 368:335-7. [PMID: 11227500 DOI: 10.1007/s002160000463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel poly(vinyl chloride) membrane electrode with dibutyl phthalate as plasticizer based on the pethidine-tetraphenylborate ion-association complex as ion-exchange site for the determination of pethidine hydrochloride in injections and tablets was developed. A linear response for 1 x 10(-5) to 1 x 10(-2) mol/L drug with a slope of 51.77 mV/decade was established. The optimum pH range was 2-8. The lower detection limit was 2.18 x 10(-6) mol/L. There were negligible interferences from a number of inorganic and organic cations and some common drug excipients. The electrode proposed had been successfully applied to determine pethidine hydrochloride in tablets and injections. The results correlated well with those obtained by the United States Pharmacopoeia standard procedure.
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Affiliation(s)
- Z H Liu
- Department of Chemistry, Yunnan University, Kunming, PR China
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Wen ML, Zhao YB, Chen X, Wang CY. Potentiometric sensor for methylene blue based on methylene blue-silicotungstate ion association and its pharmaceutical applications. J Pharm Biomed Anal 1999; 18:957-61. [PMID: 9925330 DOI: 10.1016/s0731-7085(98)00104-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A methylene blue (MB) poly(vinyl chloride) membrane sensor based on MB-silicotungstate (SLT) ion association as electroactive material was described. The linear response covered the range 1 x 10(-3)-1 x 10(-6) mol x dm(-3) MB solution, with a slope 52.0+/-0.8 mV decade(-1) (pH range 3.0-10.0). The detection limit was 7.65 x 10(-7) mol x dm(-3). The electrode showed stability, good reproducibility and fast response. Interferences from common inorganic cations, some organic base were negligible. These characteristics of the electrode enabled it to be used successfully for the determination of MB in injection. There was a good agreement for the results of MB content in injection between potentiometric method and USP standard procedure.
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Affiliation(s)
- M L Wen
- Department of Chemistry, Yunnan University, Kunmimg, People's Republic of China
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Jagoda EM, Wen ML, Yost FJ, Schreiber GJ, Tu JI. An affinity column method for determination of the immunoreactivity of 131I-chimeric L6 monoclonal antibody and comparison to in vivo tumor localization. J Immunol Methods 1994; 173:191-201. [PMID: 8046254 DOI: 10.1016/0022-1759(94)00107-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An affinity column method was developed to determine the immunoreactivity of 131I-ChiL6 (chimeric L6 monoclonal antibody), a candidate for radioimmunotherapy. This method involved assessing the binding of the radiolabeled antibody to antigen containing membranes bound to a Reacti-gel agarose matrix. The immunoreactivity determined by the affinity column method correlated to other in vitro binding assays including the Lindmo infinite antigen excess method. In tumor-bearing mice which had been injected with 131I-ChiL6, which possessed high immunoreactivities (90-82%), a high tumor uptake (13.5-10.5% ID/g) was observed. A decrease in tumor uptake (5.2-4.8% ID/g) was observed with 131I-ChiL6 samples of low immunoreactivity (42% and 31%, respectively). While a moderate loss of immunoreactivity (4-18%) of the 131I-ChiL6 samples could be detected by the affinity column method, the loss of tumor uptake in vivo observed was not as significant. This method was found to be an efficient and sensitive method for detecting damage to the antibody during radiolabeling and applicable as a quality control method for clinical trials. This rapid method, compared to the other in vitro binding assays (including the Lindmo infinite antigen excess method) has distinct advantages as a quality control method since it requires less manipulation and can be semi-automated.
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Affiliation(s)
- E M Jagoda
- Bristol-Myers Squibb Pharmaceutical Research Institute, Department of Radioimmunology, New Brunswick, NJ 08903-0191
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Alvarez VL, Wen ML, Lee C, Lopes AD, Rodwell JD, McKearn TJ. Site-specifically modified 111In labelled antibodies give low liver backgrounds and improved radioimmunoscintigraphy. Int J Rad Appl Instrum B 1986; 13:347-52. [PMID: 3793488 DOI: 10.1016/0883-2897(86)90008-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Site-specific modification of monoclonal antibodies at their oligosaccharide had previously been demonstrated to produce excellent 111In imaging in a xenograft model using a Brown Norway (BN) rat lymphoma and a rat anti-BN MHC monoclonal antibody [Lee C. et al. Fed. Proc. Abstr. 43 3014 (1984)]. These results are due, in part, to lack of liver uptake, so we wanted to evaluate the extent of hepatic uptake observed with different monoclonal antibodies in normal mice. Biodistribution data were obtained for four monoclonal antibodies by first modifying each antibody at its carbohydrate with a diethylenetriaminepentaacetic acid (DTPA) derivative. The antibodies were then labelled with 111In and injected into normal mice. Images were obtained 24 h post-injection, and at 48 h the mice were dissected and the tissue-to-blood (T:B) ratios determined. T:B ratios were approximately 1 (or less) for every organ evaluated, indicating minimal non-specific uptake into these organs. Data is also presented for the BN-rat system which shows excellent localization into the tumor xenograft and low non-specific organ uptake. These data indicate that modification of antibodies site-specifically at their oligosaccharide results in minimal non-specific uptake into non-target tissues and enhanced localization into the tumor target, and that this may represent a preferred method for production of 111In labelled antibodies.
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